Starting phenix.real_space_refine on Mon Apr 6 14:12:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nj2_49462/04_2026/9nj2_49462.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nj2_49462/04_2026/9nj2_49462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nj2_49462/04_2026/9nj2_49462.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nj2_49462/04_2026/9nj2_49462.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nj2_49462/04_2026/9nj2_49462.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nj2_49462/04_2026/9nj2_49462.map" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 9 9.91 5 S 112 5.16 5 C 11924 2.51 5 N 3268 2.21 5 O 3760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19073 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2960 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "B" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2960 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "C" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2960 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "D" Number of atoms: 2960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 2960 Classifications: {'peptide': 385} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 364} Chain: "H" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "I" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "J" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "K" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 934 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "M" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "N" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "O" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 830 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 102} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 3, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CA': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.61, per 1000 atoms: 0.24 Number of scatterers: 19073 At special positions: 0 Unit cell: (158.048, 158.048, 97.4491, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 9 19.99 S 112 16.00 O 3760 8.00 N 3268 7.00 C 11924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.05 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.10 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 231 " distance=2.07 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 238 " distance=2.10 Simple disulfide: pdb=" SG CYS A 279 " - pdb=" SG CYS A 292 " distance=2.09 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 290 " distance=2.07 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 335 " distance=2.08 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 446 " distance=2.16 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.10 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 231 " distance=2.07 Simple disulfide: pdb=" SG CYS B 233 " - pdb=" SG CYS B 238 " distance=2.10 Simple disulfide: pdb=" SG CYS B 279 " - pdb=" SG CYS B 292 " distance=2.09 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 290 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 335 " distance=2.08 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 446 " distance=2.16 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.05 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.10 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 231 " distance=2.07 Simple disulfide: pdb=" SG CYS C 233 " - pdb=" SG CYS C 238 " distance=2.10 Simple disulfide: pdb=" SG CYS C 279 " - pdb=" SG CYS C 292 " distance=2.09 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 290 " distance=2.07 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 335 " distance=2.08 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 446 " distance=2.16 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.05 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.10 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 231 " distance=2.07 Simple disulfide: pdb=" SG CYS D 233 " - pdb=" SG CYS D 238 " distance=2.10 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.09 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.07 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 335 " distance=2.08 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 446 " distance=2.16 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.07 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.07 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.07 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.05 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.05 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 501 " - " ASN A 88 " " NAG A 502 " - " ASN A 146 " " NAG A 503 " - " ASN A 235 " " NAG B 500 " - " ASN B 88 " " NAG B 501 " - " ASN B 146 " " NAG B 502 " - " ASN B 235 " " NAG C 500 " - " ASN C 88 " " NAG C 501 " - " ASN C 146 " " NAG C 502 " - " ASN C 235 " " NAG D 500 " - " ASN D 88 " " NAG D 501 " - " ASN D 146 " " NAG D 502 " - " ASN D 235 " Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 843.2 milliseconds 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4440 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 52 sheets defined 5.5% alpha, 43.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 409 through 414 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 409 through 414 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 74 through 76 No H-bonds generated for 'chain 'I' and resid 74 through 76' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 74 through 76 No H-bonds generated for 'chain 'J' and resid 74 through 76' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 74 through 76 No H-bonds generated for 'chain 'K' and resid 74 through 76' Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 79 through 83 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'O' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.381A pdb=" N SER A 444 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS A 102 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER A 442 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 124 removed outlier: 4.621A pdb=" N PHE A 115 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA A 138 " --> pdb=" O PHE A 115 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN A 136 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER A 160 " --> pdb=" O PHE A 174 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N PHE A 174 " --> pdb=" O SER A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 185 removed outlier: 6.059A pdb=" N TYR A 208 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 232 through 234 removed outlier: 7.054A pdb=" N HIS A 253 " --> pdb=" O GLU A 268 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU A 268 " --> pdb=" O HIS A 253 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE A 255 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER A 266 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS A 257 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 277 through 284 removed outlier: 5.477A pdb=" N GLU A 278 " --> pdb=" O ARG A 293 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG A 293 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 353 removed outlier: 6.750A pdb=" N SER A 369 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA A 395 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N PHE A 371 " --> pdb=" O ILE A 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.381A pdb=" N SER B 444 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS B 102 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER B 442 " --> pdb=" O LYS B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.620A pdb=" N PHE B 115 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA B 138 " --> pdb=" O PHE B 115 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN B 136 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER B 160 " --> pdb=" O PHE B 174 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE B 174 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 180 through 185 removed outlier: 6.059A pdb=" N TYR B 208 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE B 212 " --> pdb=" O TYR B 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234 removed outlier: 7.054A pdb=" N HIS B 253 " --> pdb=" O GLU B 268 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU B 268 " --> pdb=" O HIS B 253 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 255 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER B 266 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS B 257 " --> pdb=" O VAL B 264 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 277 through 284 removed outlier: 5.476A pdb=" N GLU B 278 " --> pdb=" O ARG B 293 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ARG B 293 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 353 removed outlier: 6.752A pdb=" N SER B 369 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA B 395 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE B 371 " --> pdb=" O ILE B 393 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.382A pdb=" N SER C 444 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS C 102 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N SER C 442 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 115 through 124 removed outlier: 4.619A pdb=" N PHE C 115 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ALA C 138 " --> pdb=" O PHE C 115 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN C 136 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER C 160 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N PHE C 174 " --> pdb=" O SER C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 180 through 185 removed outlier: 6.059A pdb=" N TYR C 208 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE C 212 " --> pdb=" O TYR C 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 232 through 234 removed outlier: 7.055A pdb=" N HIS C 253 " --> pdb=" O GLU C 268 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU C 268 " --> pdb=" O HIS C 253 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE C 255 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER C 266 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS C 257 " --> pdb=" O VAL C 264 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 277 through 284 removed outlier: 5.477A pdb=" N GLU C 278 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG C 293 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 350 through 353 removed outlier: 6.753A pdb=" N SER C 369 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA C 395 " --> pdb=" O SER C 369 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE C 371 " --> pdb=" O ILE C 393 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.381A pdb=" N SER D 444 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.620A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 180 through 185 removed outlier: 6.059A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 232 through 234 removed outlier: 7.054A pdb=" N HIS D 253 " --> pdb=" O GLU D 268 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLU D 268 " --> pdb=" O HIS D 253 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE D 255 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N SER D 266 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS D 257 " --> pdb=" O VAL D 264 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 277 through 284 removed outlier: 5.477A pdb=" N GLU D 278 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ARG D 293 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 350 through 353 removed outlier: 6.753A pdb=" N SER D 369 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA D 395 " --> pdb=" O SER D 369 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AC8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.606A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.596A pdb=" N SER H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AD2, first strand: chain 'I' and resid 4 through 6 Processing sheet with id=AD3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.606A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.596A pdb=" N SER I 117 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 104 through 105 Processing sheet with id=AD6, first strand: chain 'J' and resid 4 through 6 Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.606A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.596A pdb=" N SER J 117 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 104 through 105 Processing sheet with id=AE1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.607A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.596A pdb=" N SER K 117 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 104 through 105 Processing sheet with id=AE5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.548A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.515A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.548A pdb=" N LEU M 33 " --> pdb=" O TYR M 49 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.516A pdb=" N THR M 98 " --> pdb=" O GLN M 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.548A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.515A pdb=" N THR N 98 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.548A pdb=" N LEU O 33 " --> pdb=" O TYR O 49 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR O 49 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP O 35 " --> pdb=" O LEU O 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.516A pdb=" N THR O 98 " --> pdb=" O GLN O 90 " (cutoff:3.500A) 752 hydrogen bonds defined for protein. 1812 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.96 Time building geometry restraints manager: 2.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4469 1.33 - 1.45: 6178 1.45 - 1.58: 8773 1.58 - 1.70: 0 1.70 - 1.82: 140 Bond restraints: 19560 Sorted by residual: bond pdb=" CA SER A 456 " pdb=" CB SER A 456 " ideal model delta sigma weight residual 1.529 1.464 0.065 1.38e-02 5.25e+03 2.19e+01 bond pdb=" CA SER B 456 " pdb=" CB SER B 456 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.38e-02 5.25e+03 2.15e+01 bond pdb=" CA SER C 456 " pdb=" CB SER C 456 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.38e-02 5.25e+03 2.13e+01 bond pdb=" CA SER D 456 " pdb=" CB SER D 456 " ideal model delta sigma weight residual 1.529 1.465 0.064 1.38e-02 5.25e+03 2.13e+01 bond pdb=" CA SER A 172 " pdb=" CB SER A 172 " ideal model delta sigma weight residual 1.530 1.464 0.066 1.48e-02 4.57e+03 1.98e+01 ... (remaining 19555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 20937 1.77 - 3.54: 4719 3.54 - 5.30: 774 5.30 - 7.07: 130 7.07 - 8.84: 32 Bond angle restraints: 26592 Sorted by residual: angle pdb=" CA PHE D 406 " pdb=" CB PHE D 406 " pdb=" CG PHE D 406 " ideal model delta sigma weight residual 113.80 119.82 -6.02 1.00e+00 1.00e+00 3.62e+01 angle pdb=" CA PHE H 115 " pdb=" CB PHE H 115 " pdb=" CG PHE H 115 " ideal model delta sigma weight residual 113.80 107.79 6.01 1.00e+00 1.00e+00 3.62e+01 angle pdb=" CA PHE K 115 " pdb=" CB PHE K 115 " pdb=" CG PHE K 115 " ideal model delta sigma weight residual 113.80 107.79 6.01 1.00e+00 1.00e+00 3.62e+01 angle pdb=" CA PHE J 115 " pdb=" CB PHE J 115 " pdb=" CG PHE J 115 " ideal model delta sigma weight residual 113.80 107.79 6.01 1.00e+00 1.00e+00 3.62e+01 angle pdb=" CA PHE B 406 " pdb=" CB PHE B 406 " pdb=" CG PHE B 406 " ideal model delta sigma weight residual 113.80 119.80 -6.00 1.00e+00 1.00e+00 3.60e+01 ... (remaining 26587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.22: 10888 16.22 - 32.43: 555 32.43 - 48.65: 104 48.65 - 64.87: 49 64.87 - 81.09: 20 Dihedral angle restraints: 11616 sinusoidal: 4644 harmonic: 6972 Sorted by residual: dihedral pdb=" CA THR B 226 " pdb=" C THR B 226 " pdb=" N GLN B 227 " pdb=" CA GLN B 227 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA THR D 226 " pdb=" C THR D 226 " pdb=" N GLN D 227 " pdb=" CA GLN D 227 " ideal model delta harmonic sigma weight residual 180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA THR C 226 " pdb=" C THR C 226 " pdb=" N GLN C 227 " pdb=" CA GLN C 227 " ideal model delta harmonic sigma weight residual -180.00 -157.05 -22.95 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 11613 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.250: 2840 0.250 - 0.500: 16 0.500 - 0.750: 0 0.750 - 1.000: 0 1.000 - 1.251: 4 Chirality restraints: 2860 Sorted by residual: chirality pdb=" C1 NAG A 503 " pdb=" ND2 ASN A 235 " pdb=" C2 NAG A 503 " pdb=" O5 NAG A 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.15 -1.25 2.00e-01 2.50e+01 3.91e+01 chirality pdb=" C1 NAG C 502 " pdb=" ND2 ASN C 235 " pdb=" C2 NAG C 502 " pdb=" O5 NAG C 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.15 -1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" C1 NAG B 502 " pdb=" ND2 ASN B 235 " pdb=" C2 NAG B 502 " pdb=" O5 NAG B 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.15 -1.25 2.00e-01 2.50e+01 3.88e+01 ... (remaining 2857 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 235 " 0.133 2.00e-02 2.50e+03 2.51e-01 7.89e+02 pdb=" CG ASN B 235 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 235 " 0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN B 235 " -0.456 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.292 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 235 " -0.133 2.00e-02 2.50e+03 2.51e-01 7.88e+02 pdb=" CG ASN D 235 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN D 235 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN D 235 " 0.456 2.00e-02 2.50e+03 pdb=" C1 NAG D 502 " -0.292 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 235 " -0.133 2.00e-02 2.50e+03 2.50e-01 7.84e+02 pdb=" CG ASN C 235 " 0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 235 " -0.060 2.00e-02 2.50e+03 pdb=" ND2 ASN C 235 " 0.455 2.00e-02 2.50e+03 pdb=" C1 NAG C 502 " -0.291 2.00e-02 2.50e+03 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 444 2.65 - 3.21: 17170 3.21 - 3.77: 30956 3.77 - 4.34: 46776 4.34 - 4.90: 74761 Nonbonded interactions: 170107 Sorted by model distance: nonbonded pdb=" OD1 ASP A 384 " pdb="CA CA A 505 " model vdw 2.087 2.510 nonbonded pdb=" OD1 ASP C 384 " pdb="CA CA C 504 " model vdw 2.087 2.510 nonbonded pdb=" OD1 ASP D 384 " pdb="CA CA D 504 " model vdw 2.088 2.510 nonbonded pdb=" OD1 ASP B 384 " pdb="CA CA B 504 " model vdw 2.088 2.510 nonbonded pdb=" O TYR D 344 " pdb="CA CA D 503 " model vdw 2.203 2.510 ... (remaining 170102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 83 through 505) selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.150 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.132 19612 Z= 0.689 Angle : 1.570 8.841 26708 Z= 1.014 Chirality : 0.098 1.251 2860 Planarity : 0.016 0.239 3432 Dihedral : 11.367 81.086 7056 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.51 % Favored : 97.16 % Rotamer: Outliers : 0.96 % Allowed : 1.73 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.16), residues: 2428 helix: -0.68 (0.86), residues: 24 sheet: 0.67 (0.16), residues: 976 loop : -0.34 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.003 ARG B 107 TYR 0.036 0.007 TYR B 276 PHE 0.051 0.009 PHE C 349 TRP 0.061 0.009 TRP B 457 HIS 0.012 0.003 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.01066 (19560) covalent geometry : angle 1.55422 (26592) SS BOND : bond 0.06185 ( 40) SS BOND : angle 3.50674 ( 80) hydrogen bonds : bond 0.16801 ( 696) hydrogen bonds : angle 8.10580 ( 1812) link_NAG-ASN : bond 0.01029 ( 12) link_NAG-ASN : angle 4.20956 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 296 time to evaluate : 0.667 Fit side-chains REVERT: A 262 LYS cc_start: 0.8372 (mttt) cc_final: 0.7861 (mttt) REVERT: A 309 ASN cc_start: 0.7990 (m-40) cc_final: 0.7589 (t0) REVERT: A 462 GLU cc_start: 0.8569 (tt0) cc_final: 0.8211 (tm-30) REVERT: B 262 LYS cc_start: 0.8372 (mttt) cc_final: 0.7862 (mttt) REVERT: B 309 ASN cc_start: 0.7982 (m-40) cc_final: 0.7580 (t0) REVERT: B 462 GLU cc_start: 0.8565 (tt0) cc_final: 0.8158 (tm-30) REVERT: C 262 LYS cc_start: 0.8372 (mttt) cc_final: 0.7860 (mttt) REVERT: C 309 ASN cc_start: 0.7984 (m-40) cc_final: 0.7583 (t0) REVERT: C 462 GLU cc_start: 0.8570 (tt0) cc_final: 0.8213 (tm-30) REVERT: D 262 LYS cc_start: 0.8374 (mttt) cc_final: 0.7861 (mttm) REVERT: D 309 ASN cc_start: 0.7976 (m-40) cc_final: 0.7577 (t0) REVERT: D 462 GLU cc_start: 0.8569 (tt0) cc_final: 0.8162 (tm-30) REVERT: H 73 ASP cc_start: 0.5960 (t0) cc_final: 0.5678 (p0) REVERT: H 77 THR cc_start: 0.7390 (m) cc_final: 0.7180 (t) REVERT: H 98 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7982 (ttm-80) REVERT: H 111 GLU cc_start: 0.8817 (mt-10) cc_final: 0.8520 (mm-30) REVERT: I 73 ASP cc_start: 0.5960 (t0) cc_final: 0.5679 (p0) REVERT: I 77 THR cc_start: 0.7394 (m) cc_final: 0.7183 (t) REVERT: I 98 ARG cc_start: 0.8321 (ttm-80) cc_final: 0.7984 (ttm-80) REVERT: I 111 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8517 (mm-30) REVERT: J 73 ASP cc_start: 0.5957 (t0) cc_final: 0.5676 (p0) REVERT: J 77 THR cc_start: 0.7389 (m) cc_final: 0.7178 (t) REVERT: J 98 ARG cc_start: 0.8320 (ttm-80) cc_final: 0.7983 (ttm-80) REVERT: J 111 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8554 (mm-30) REVERT: K 73 ASP cc_start: 0.5959 (t0) cc_final: 0.5676 (p0) REVERT: K 77 THR cc_start: 0.7390 (m) cc_final: 0.7184 (t) REVERT: K 98 ARG cc_start: 0.8318 (ttm-80) cc_final: 0.7981 (ttm-80) REVERT: K 111 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8518 (mm-30) REVERT: L 82 ASP cc_start: 0.8568 (m-30) cc_final: 0.8331 (m-30) REVERT: L 104 LYS cc_start: 0.8087 (tttt) cc_final: 0.7739 (mtpm) REVERT: M 82 ASP cc_start: 0.8568 (m-30) cc_final: 0.8332 (m-30) REVERT: M 104 LYS cc_start: 0.8058 (tttt) cc_final: 0.7706 (mtpm) REVERT: N 82 ASP cc_start: 0.8569 (m-30) cc_final: 0.8333 (m-30) REVERT: N 104 LYS cc_start: 0.8087 (tttt) cc_final: 0.7739 (mtpm) REVERT: O 82 ASP cc_start: 0.8569 (m-30) cc_final: 0.8333 (m-30) REVERT: O 104 LYS cc_start: 0.8048 (tttt) cc_final: 0.7681 (mtpm) outliers start: 20 outliers final: 0 residues processed: 316 average time/residue: 0.6944 time to fit residues: 244.6922 Evaluate side-chains 233 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN C 95 ASN D 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.120224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.089845 restraints weight = 19242.959| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.29 r_work: 0.2900 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19612 Z= 0.135 Angle : 0.637 8.413 26708 Z= 0.341 Chirality : 0.047 0.261 2860 Planarity : 0.004 0.027 3432 Dihedral : 6.121 40.342 2896 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 1.81 % Favored : 98.02 % Rotamer: Outliers : 0.87 % Allowed : 6.07 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.17), residues: 2428 helix: -0.18 (1.02), residues: 24 sheet: 0.73 (0.16), residues: 1032 loop : 0.11 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.011 0.001 TYR A 274 PHE 0.017 0.002 PHE D 406 TRP 0.019 0.002 TRP B 179 HIS 0.002 0.001 HIS A 155 Details of bonding type rmsd covalent geometry : bond 0.00280 (19560) covalent geometry : angle 0.60668 (26592) SS BOND : bond 0.00358 ( 40) SS BOND : angle 2.00694 ( 80) hydrogen bonds : bond 0.04454 ( 696) hydrogen bonds : angle 6.34828 ( 1812) link_NAG-ASN : bond 0.00750 ( 12) link_NAG-ASN : angle 4.45980 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 263 time to evaluate : 0.748 Fit side-chains REVERT: A 262 LYS cc_start: 0.8457 (mttt) cc_final: 0.8144 (mttm) REVERT: A 462 GLU cc_start: 0.8294 (tt0) cc_final: 0.8081 (tm-30) REVERT: B 173 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7912 (ttm170) REVERT: B 262 LYS cc_start: 0.8444 (mttt) cc_final: 0.8139 (mttm) REVERT: C 173 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7920 (ttm170) REVERT: C 262 LYS cc_start: 0.8444 (mttt) cc_final: 0.8135 (mttm) REVERT: C 462 GLU cc_start: 0.8309 (tt0) cc_final: 0.8089 (tm-30) REVERT: D 173 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7920 (ttm170) REVERT: D 262 LYS cc_start: 0.8453 (mttt) cc_final: 0.8144 (mttm) outliers start: 18 outliers final: 3 residues processed: 267 average time/residue: 0.7140 time to fit residues: 212.1713 Evaluate side-chains 235 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 229 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 11 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 177 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 190 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 116 optimal weight: 0.2980 chunk 124 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.087309 restraints weight = 19438.558| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 1.34 r_work: 0.2844 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19612 Z= 0.158 Angle : 0.605 5.673 26708 Z= 0.328 Chirality : 0.046 0.178 2860 Planarity : 0.004 0.029 3432 Dihedral : 5.740 33.830 2896 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 1.25 % Allowed : 6.70 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.17), residues: 2428 helix: -0.24 (1.04), residues: 24 sheet: 0.70 (0.15), residues: 1028 loop : 0.17 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 156 TYR 0.014 0.002 TYR A 274 PHE 0.017 0.002 PHE D 406 TRP 0.012 0.001 TRP B 179 HIS 0.003 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00334 (19560) covalent geometry : angle 0.58737 (26592) SS BOND : bond 0.00508 ( 40) SS BOND : angle 1.55820 ( 80) hydrogen bonds : bond 0.04450 ( 696) hydrogen bonds : angle 6.10344 ( 1812) link_NAG-ASN : bond 0.00410 ( 12) link_NAG-ASN : angle 3.32480 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.671 Fit side-chains REVERT: A 262 LYS cc_start: 0.8458 (mttt) cc_final: 0.8136 (mttm) REVERT: A 462 GLU cc_start: 0.8319 (tt0) cc_final: 0.8061 (tm-30) REVERT: B 262 LYS cc_start: 0.8457 (mttt) cc_final: 0.8135 (mttm) REVERT: B 462 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: C 262 LYS cc_start: 0.8448 (mttt) cc_final: 0.8128 (mttm) REVERT: C 462 GLU cc_start: 0.8330 (tt0) cc_final: 0.8065 (tm-30) REVERT: D 262 LYS cc_start: 0.8454 (mttt) cc_final: 0.8130 (mttm) REVERT: D 462 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: H 81 MET cc_start: 0.8776 (tmm) cc_final: 0.8475 (tmm) REVERT: I 81 MET cc_start: 0.8780 (tmm) cc_final: 0.8478 (tmm) REVERT: J 81 MET cc_start: 0.8765 (tmm) cc_final: 0.8461 (tmm) REVERT: K 81 MET cc_start: 0.8763 (tmm) cc_final: 0.8461 (tmm) outliers start: 26 outliers final: 8 residues processed: 232 average time/residue: 0.7732 time to fit residues: 198.3326 Evaluate side-chains 206 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 71 optimal weight: 0.9980 chunk 180 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 223 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 211 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN H 62 GLN I 62 GLN J 62 GLN K 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.085115 restraints weight = 19522.655| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.35 r_work: 0.2822 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19612 Z= 0.222 Angle : 0.661 6.330 26708 Z= 0.359 Chirality : 0.049 0.274 2860 Planarity : 0.004 0.035 3432 Dihedral : 6.228 43.063 2896 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.87 % Rotamer: Outliers : 1.06 % Allowed : 6.65 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2428 helix: -0.78 (0.94), residues: 24 sheet: 0.57 (0.15), residues: 1008 loop : 0.07 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 156 TYR 0.017 0.002 TYR B 274 PHE 0.018 0.003 PHE A 406 TRP 0.012 0.002 TRP B 179 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00484 (19560) covalent geometry : angle 0.64382 (26592) SS BOND : bond 0.00609 ( 40) SS BOND : angle 2.01526 ( 80) hydrogen bonds : bond 0.04815 ( 696) hydrogen bonds : angle 6.27376 ( 1812) link_NAG-ASN : bond 0.00505 ( 12) link_NAG-ASN : angle 3.01051 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.696 Fit side-chains REVERT: A 462 GLU cc_start: 0.8324 (tt0) cc_final: 0.8049 (tm-30) REVERT: B 262 LYS cc_start: 0.8458 (mttt) cc_final: 0.8139 (mttm) REVERT: B 462 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: C 462 GLU cc_start: 0.8320 (tt0) cc_final: 0.8042 (tm-30) REVERT: D 262 LYS cc_start: 0.8450 (mttt) cc_final: 0.8135 (mttm) REVERT: D 462 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7768 (tm-30) outliers start: 22 outliers final: 12 residues processed: 245 average time/residue: 0.6785 time to fit residues: 185.5152 Evaluate side-chains 235 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 221 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 97 optimal weight: 8.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.084680 restraints weight = 19512.493| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 1.34 r_work: 0.2774 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 19612 Z= 0.308 Angle : 0.737 6.930 26708 Z= 0.400 Chirality : 0.053 0.330 2860 Planarity : 0.005 0.046 3432 Dihedral : 6.852 49.747 2896 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.38 % Rotamer: Outliers : 0.92 % Allowed : 7.47 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.17), residues: 2428 helix: -1.01 (0.88), residues: 24 sheet: 0.39 (0.16), residues: 996 loop : -0.01 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 156 TYR 0.020 0.002 TYR B 274 PHE 0.021 0.003 PHE A 349 TRP 0.014 0.002 TRP A 457 HIS 0.006 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00680 (19560) covalent geometry : angle 0.71997 (26592) SS BOND : bond 0.00775 ( 40) SS BOND : angle 2.25168 ( 80) hydrogen bonds : bond 0.05291 ( 696) hydrogen bonds : angle 6.41387 ( 1812) link_NAG-ASN : bond 0.00696 ( 12) link_NAG-ASN : angle 3.05830 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 223 time to evaluate : 0.729 Fit side-chains REVERT: A 262 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8317 (mttm) REVERT: A 462 GLU cc_start: 0.8359 (tt0) cc_final: 0.8110 (tm-30) REVERT: B 262 LYS cc_start: 0.8513 (mttt) cc_final: 0.8117 (mttm) REVERT: B 462 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: C 262 LYS cc_start: 0.8605 (mtmt) cc_final: 0.8309 (mttm) REVERT: C 462 GLU cc_start: 0.8351 (tt0) cc_final: 0.8102 (tm-30) REVERT: D 262 LYS cc_start: 0.8515 (mttt) cc_final: 0.8116 (mttm) REVERT: D 462 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7779 (tm-30) REVERT: H 81 MET cc_start: 0.8865 (tmm) cc_final: 0.8618 (tmm) REVERT: I 81 MET cc_start: 0.8873 (tmm) cc_final: 0.8627 (tmm) REVERT: J 81 MET cc_start: 0.8867 (tmm) cc_final: 0.8624 (tmm) REVERT: K 81 MET cc_start: 0.8863 (tmm) cc_final: 0.8612 (tmm) outliers start: 19 outliers final: 13 residues processed: 239 average time/residue: 0.7195 time to fit residues: 191.1602 Evaluate side-chains 230 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 27 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 21 optimal weight: 6.9990 chunk 239 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.086129 restraints weight = 19457.850| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.29 r_work: 0.2796 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 2.49 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 19612 Z= 0.217 Angle : 0.654 6.687 26708 Z= 0.354 Chirality : 0.049 0.256 2860 Planarity : 0.004 0.033 3432 Dihedral : 6.524 45.854 2896 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.29 % Favored : 96.54 % Rotamer: Outliers : 0.92 % Allowed : 8.24 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.17), residues: 2428 helix: -0.95 (0.87), residues: 24 sheet: 0.36 (0.16), residues: 996 loop : -0.01 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 156 TYR 0.013 0.002 TYR B 274 PHE 0.017 0.003 PHE A 406 TRP 0.014 0.002 TRP D 179 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00472 (19560) covalent geometry : angle 0.63950 (26592) SS BOND : bond 0.00572 ( 40) SS BOND : angle 1.84652 ( 80) hydrogen bonds : bond 0.04726 ( 696) hydrogen bonds : angle 6.24815 ( 1812) link_NAG-ASN : bond 0.00474 ( 12) link_NAG-ASN : angle 2.77140 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 229 time to evaluate : 0.723 Fit side-chains REVERT: A 262 LYS cc_start: 0.8553 (mtmt) cc_final: 0.8260 (mttm) REVERT: A 462 GLU cc_start: 0.8337 (tt0) cc_final: 0.8092 (tm-30) REVERT: B 262 LYS cc_start: 0.8496 (mttt) cc_final: 0.8285 (mtmt) REVERT: B 462 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7769 (tm-30) REVERT: C 262 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8248 (mttm) REVERT: C 462 GLU cc_start: 0.8335 (tt0) cc_final: 0.8085 (tm-30) REVERT: D 262 LYS cc_start: 0.8512 (mttt) cc_final: 0.8297 (mtmt) REVERT: D 462 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7766 (tm-30) outliers start: 19 outliers final: 12 residues processed: 245 average time/residue: 0.7114 time to fit residues: 194.1823 Evaluate side-chains 237 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 206 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 89 optimal weight: 0.5980 chunk 239 optimal weight: 0.9990 chunk 165 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.119883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.089349 restraints weight = 19590.625| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.34 r_work: 0.2883 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19612 Z= 0.110 Angle : 0.544 6.390 26708 Z= 0.294 Chirality : 0.045 0.183 2860 Planarity : 0.003 0.031 3432 Dihedral : 5.471 38.770 2896 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Rotamer: Outliers : 1.25 % Allowed : 8.43 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2428 helix: -0.20 (1.05), residues: 24 sheet: 0.47 (0.16), residues: 996 loop : 0.10 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 361 TYR 0.008 0.001 TYR K 95 PHE 0.015 0.002 PHE B 406 TRP 0.015 0.001 TRP D 179 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00226 (19560) covalent geometry : angle 0.53448 (26592) SS BOND : bond 0.00318 ( 40) SS BOND : angle 1.28384 ( 80) hydrogen bonds : bond 0.03670 ( 696) hydrogen bonds : angle 5.90082 ( 1812) link_NAG-ASN : bond 0.00198 ( 12) link_NAG-ASN : angle 2.15979 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.806 Fit side-chains REVERT: A 262 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8119 (ttpp) REVERT: A 462 GLU cc_start: 0.8380 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 462 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: C 262 LYS cc_start: 0.8433 (mtmt) cc_final: 0.8108 (ttpp) REVERT: C 462 GLU cc_start: 0.8372 (tt0) cc_final: 0.8154 (tm-30) REVERT: D 462 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7767 (tm-30) REVERT: H 81 MET cc_start: 0.8813 (tmm) cc_final: 0.8551 (tmm) REVERT: I 81 MET cc_start: 0.8829 (tmm) cc_final: 0.8567 (tmm) REVERT: J 81 MET cc_start: 0.8832 (tmm) cc_final: 0.8576 (tmm) REVERT: K 81 MET cc_start: 0.8823 (tmm) cc_final: 0.8561 (tmm) outliers start: 26 outliers final: 12 residues processed: 263 average time/residue: 0.6854 time to fit residues: 200.8912 Evaluate side-chains 253 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 69 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.084609 restraints weight = 19580.987| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.35 r_work: 0.2802 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19612 Z= 0.252 Angle : 0.692 9.243 26708 Z= 0.372 Chirality : 0.050 0.328 2860 Planarity : 0.005 0.037 3432 Dihedral : 6.248 51.963 2896 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.46 % Favored : 96.38 % Rotamer: Outliers : 0.87 % Allowed : 8.62 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2428 helix: -0.66 (0.92), residues: 24 sheet: 0.41 (0.16), residues: 992 loop : 0.07 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 156 TYR 0.014 0.002 TYR B 274 PHE 0.018 0.003 PHE B 406 TRP 0.012 0.002 TRP C 457 HIS 0.005 0.001 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00556 (19560) covalent geometry : angle 0.67285 (26592) SS BOND : bond 0.00744 ( 40) SS BOND : angle 2.46615 ( 80) hydrogen bonds : bond 0.04825 ( 696) hydrogen bonds : angle 6.21005 ( 1812) link_NAG-ASN : bond 0.00468 ( 12) link_NAG-ASN : angle 2.76223 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.633 Fit side-chains REVERT: A 262 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8264 (mttm) REVERT: B 462 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7785 (tm-30) REVERT: C 262 LYS cc_start: 0.8550 (mtmt) cc_final: 0.8253 (mttm) REVERT: D 462 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: H 81 MET cc_start: 0.8853 (tmm) cc_final: 0.8563 (tmm) REVERT: I 81 MET cc_start: 0.8862 (tmm) cc_final: 0.8571 (tmm) REVERT: J 81 MET cc_start: 0.8860 (tmm) cc_final: 0.8569 (tmm) REVERT: K 81 MET cc_start: 0.8858 (tmm) cc_final: 0.8566 (tmm) outliers start: 18 outliers final: 16 residues processed: 235 average time/residue: 0.7874 time to fit residues: 204.7137 Evaluate side-chains 234 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 48 ILE Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 48 ILE Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 48 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 189 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 179 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 239 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN H 39 GLN K 39 GLN L 38 GLN O 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.120872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.090654 restraints weight = 19497.796| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.33 r_work: 0.2909 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19612 Z= 0.103 Angle : 0.545 7.780 26708 Z= 0.292 Chirality : 0.045 0.226 2860 Planarity : 0.003 0.031 3432 Dihedral : 5.328 47.733 2896 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.64 % Favored : 97.20 % Rotamer: Outliers : 0.77 % Allowed : 9.34 % Favored : 89.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2428 helix: -0.02 (1.09), residues: 24 sheet: 0.49 (0.16), residues: 1048 loop : 0.12 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 61 TYR 0.009 0.001 TYR H 95 PHE 0.015 0.002 PHE C 406 TRP 0.016 0.001 TRP B 179 HIS 0.002 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00217 (19560) covalent geometry : angle 0.53324 (26592) SS BOND : bond 0.00460 ( 40) SS BOND : angle 1.67225 ( 80) hydrogen bonds : bond 0.03446 ( 696) hydrogen bonds : angle 5.83477 ( 1812) link_NAG-ASN : bond 0.00158 ( 12) link_NAG-ASN : angle 2.00964 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.773 Fit side-chains REVERT: A 262 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8120 (ttpp) REVERT: B 262 LYS cc_start: 0.8472 (mtmt) cc_final: 0.8102 (ttpt) REVERT: B 462 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7799 (tm-30) REVERT: C 262 LYS cc_start: 0.8421 (mtmt) cc_final: 0.8110 (ttpp) REVERT: D 262 LYS cc_start: 0.8480 (mtmt) cc_final: 0.8108 (ttpt) REVERT: D 462 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: H 81 MET cc_start: 0.8814 (tmm) cc_final: 0.8505 (tmm) REVERT: I 81 MET cc_start: 0.8819 (tmm) cc_final: 0.8511 (tmm) REVERT: J 81 MET cc_start: 0.8825 (tmm) cc_final: 0.8515 (tmm) REVERT: K 81 MET cc_start: 0.8815 (tmm) cc_final: 0.8502 (tmm) outliers start: 16 outliers final: 4 residues processed: 250 average time/residue: 0.7172 time to fit residues: 199.6307 Evaluate side-chains 244 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 238 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 181 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 220 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 202 optimal weight: 8.9990 chunk 112 optimal weight: 2.9990 chunk 114 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN K 39 GLN O 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.085459 restraints weight = 19632.460| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 1.36 r_work: 0.2768 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 19612 Z= 0.339 Angle : 0.757 9.142 26708 Z= 0.407 Chirality : 0.054 0.336 2860 Planarity : 0.005 0.047 3432 Dihedral : 6.478 53.456 2896 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.79 % Favored : 96.05 % Rotamer: Outliers : 0.67 % Allowed : 10.02 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.17), residues: 2428 helix: -0.70 (0.89), residues: 24 sheet: 0.28 (0.15), residues: 1016 loop : 0.02 (0.17), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 156 TYR 0.018 0.002 TYR D 274 PHE 0.021 0.003 PHE A 349 TRP 0.014 0.002 TRP D 457 HIS 0.005 0.002 HIS B 253 Details of bonding type rmsd covalent geometry : bond 0.00754 (19560) covalent geometry : angle 0.73755 (26592) SS BOND : bond 0.00844 ( 40) SS BOND : angle 2.48666 ( 80) hydrogen bonds : bond 0.05290 ( 696) hydrogen bonds : angle 6.32446 ( 1812) link_NAG-ASN : bond 0.00607 ( 12) link_NAG-ASN : angle 3.04754 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4856 Ramachandran restraints generated. 2428 Oldfield, 0 Emsley, 2428 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 223 time to evaluate : 0.672 Fit side-chains REVERT: A 262 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8361 (mttm) REVERT: B 262 LYS cc_start: 0.8565 (mtmt) cc_final: 0.8262 (mttm) REVERT: B 462 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: C 262 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8355 (mttm) REVERT: D 262 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8267 (mttm) REVERT: D 462 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7813 (tm-30) outliers start: 14 outliers final: 12 residues processed: 235 average time/residue: 0.7721 time to fit residues: 200.3589 Evaluate side-chains 230 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 216 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain D residue 462 GLU Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain I residue 35 SER Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain K residue 35 SER Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain M residue 29 VAL Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain O residue 29 VAL Chi-restraints excluded: chain O residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 128 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN B 308 GLN C 308 GLN D 308 GLN K 39 GLN O 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.089251 restraints weight = 19670.291| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.34 r_work: 0.2901 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 19612 Z= 0.116 Angle : 0.565 7.674 26708 Z= 0.303 Chirality : 0.046 0.234 2860 Planarity : 0.004 0.030 3432 Dihedral : 5.540 48.472 2896 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.47 % Favored : 97.36 % Rotamer: Outliers : 0.29 % Allowed : 10.98 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.17), residues: 2428 helix: -0.17 (1.04), residues: 24 sheet: 0.39 (0.16), residues: 1024 loop : 0.14 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG N 61 TYR 0.009 0.001 TYR K 95 PHE 0.015 0.002 PHE D 406 TRP 0.015 0.001 TRP D 179 HIS 0.002 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00244 (19560) covalent geometry : angle 0.55341 (26592) SS BOND : bond 0.00463 ( 40) SS BOND : angle 1.62214 ( 80) hydrogen bonds : bond 0.03640 ( 696) hydrogen bonds : angle 5.89756 ( 1812) link_NAG-ASN : bond 0.00177 ( 12) link_NAG-ASN : angle 2.12071 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7920.76 seconds wall clock time: 135 minutes 28.04 seconds (8128.04 seconds total)